Molecular interactions between ribosomal proteins. An inspection of S3-S4, S4-S5, and S4-S20 mixtures

Ribosomal proteins: their structure and spatial arrangement in prokaryotic ribosomes

During the last 15 years of ribosomal protein study, enormous progress has been made. Each of the proteins from E. coli ribosomes has been isolated, sequenced, and immunologically and physically characterized. Ribosomal proteins from other sources (e.g., from some bacteria, yeast, and rat) have been isolated and studied as well. Several proteins have recently been crystallized, and from the X-ray studies it is expected that much important information on the three-dimensional structure will be forthcoming. Many other proteins can probably be crystallized if suitable preparative procedures and crystallization conditions are found. Tremendous progress has also been made in deciphering the architecture of the ribosome. A battery of different methods has been used to provide the nearest neighbor distances of the ribosomal proteins in situ. Definitive measurements are now emanating from neutron-scattering experiments which also promise to give reasonably accurate radii of gyration of the proteins in situ. In turn, refined immune electron microscopy results supplement the neutron-scattering data and also position the proteins on the subunits themselves. This cannot be done by the other methods. Determination of the three-dimensional RNA structure within the ribosome is still in its infancy. Nonetheless, it is expected that by combining the data from protein-RNA and from RNA-RNA cross-linking studies, the structure of the RNA in situ can be unraveled. Of great interest is the fact that ribosomal subunits and ribosomes themselves have now been crystallized, and low-resolution structural maps have already been obtained. However, to grow suitable crystals and to resolve the ribosomal structure at a sufficiently high resolution remains a great challenge and task to biochemists and crystallographers.

Polynucleotide . ribosomal-protein complexes and their decoding properties

Polyadenylic acid, polycytidylic acid, polyuridylic acid or phage MS2 RNA, immobilized on Sepharose, form a complex with Escherichia coli ribosomal proteins. Regardless of their particular nucleotide composition, all four polynucleotides bind an invariable set of proteins consisting of S1, S3, S4, S5, S9, S13, L2 and L17. We found that these polynucleotide . protein complexes bind tRNA. Furthermore, it was possible to show that the poly(A) . protein and poly(U) . protein complexes select efficiently their cognate tRNAs, tRNALys and tRNAPhe respectively. This important functional property of the polynucleotide . protein complexes suggests that these ribosomal proteins belong in the ribosome to a functional domain responsible for the decoding of mRNA.

A new method for the purification of 30S ribosomal proteins from Escherichia coli using nondenaturing conditions

A new method for the purification of Escherichia coli (A19) 30S ribosomal proteins has been developed that avoids the use of denaturing conditions such as urea, acetic acid, and lyophilization. In this way the majority of the proteins from the small ribosomal subunit can be obtained in 5--100 mg quantities and at greater than or equal to 90% purity. This has been achieved by the initial "splitting" of the proteins into two main groups with LiCl followed by fractionating on ion-exchange and gel-filtration columns, in the absence of urea and in the presence of salt. The proteins prepared by this nondenaturing procedure were soluble at high ionic strength and less soluble, being aggregated, at low salt concentrations. This behavior was exactly the opposite of that exhibited by proteins prepared with methods using denaturing conditions. These new methods have enabled additional ribosomal RNA-binding proteins to be found and potential protein-proteins complexes to be isolated. Preliminary evidence that these proteins may retain a more native structure is presented.